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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcatgttccttactttgtttggataaatgtagcatatttttctacagaattttgaatttctacgaatggttattgacagttttttgatatttacatag

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 9
GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcatgttcc---ttactttgtttggataaatgtagcatatttttctacagaattttgaatttctacgaatggttattgacagttttttgatatttacatag
||||||||| |||||||||||||||||||||||||||| ||||||||||| |||||||| ||||| |||||||||||||||||||||||||||||||| ||||   ||||||  |   || | ||||   | |       | | | ||   ||   ||  ||   |    || |||   | | |                       
GCCATGCAGTTGCGCAAGTGCTGCAACCATCCATATTTATTCCAAGGAGCAGAACCTGGTCCACCTTACACAACTGGTGAACATCTAGTTGAGAATGCTGgtatgttcatgtcacaatttccattgtactgttgccaaaggtacagttcaatatttaaccttccctcctcac-aatatctgtag-----------------------

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 9
lower sequence: 13113.m00246 (Oryza sativa), 5'ss of exon 9
GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcatgttcc---ttactttgtttggataaatgtagcatatttttctacagaattttgaatttctacgaatggttattgacagttttttgatatttacatag
||||||||| |||| ||||||||||||||||||||||| ||||||||||| |||||||| ||||| |||||||||||||||||||||||||||||||| ||||   ||||||  |   || | ||||   | |       | | | ||   ||   ||  ||   |    || |||   | | |                       
GCCATGCAGTTGCGTAAGTGCTGCAACCATCCATATTTATTCCAAGGAGCAGAACCTGGTCCACCTTACACAACTGGTGAACATCTAGTTGAGAATGCTGgtatgttcatgtcacaatttccattgtactgttgccaaaggtacagttcaatatttaaccttccctcctcac-aatatctgtag-----------------------

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 9
GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcatgttccttactttgtttggataaatgtagcatatttttctacagaattttgaatttctacgaatggttattgacagttttttgatatttacatag
||||||||  |||| ||||||||||||||||||||||| |||||||| ||||| ||||| |||||||| || ||||| || |||||| |||||||||||||||  ||    | |  |    | ||||    ||| | | |  | ||||| ||  | |    ||        ||| | ||  ||  || ||| | |         
GCCATGCAATTGCGGAAGTGCTGCAACCATCCATATTTATTCCAAGGTGCTGAGCCTGGTCCACCCTATACCACTGGAGACCATCTAATTGAGAATGCAGgtactatt-catccactctagtatttgtcataatttggtac-tatttctgcaatactgcacat--------atgatcatgcactcttattttacag--------

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 9
GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcatgttccttactttgtttggataaatgtagcatat-ttttctacagaattttgaatttctacgaatggttattgacagttttttga-tatttacatag---
|| ||||| || ||||| || || || ||||||||| | |||||||| ||||||||||| || |||| ||| || || || |||||| |||| ||||| |||||  ||    | | ||| ||     || | ||   ||| |  || | |  ||  |  |||||     |  | | | |||  | ||| |   | |||||   |     
GCTATGCAACTACGCAAATGTTGTAATCATCCATATCTTTTCCAAGGTGCTGAACCTGGTCCTCCCTTCACTACAGGAGATCATCTAATTGAAAATGCTGgtaaactc----tacatacatta---agagagatactgcagacgttctttttaggttgatgaataaaatctga-gatcatttcctgttgtaaaaatattttgtttccag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 9
lower sequence: EDP05471 (Chlamydomonas reinhardtii), 5'ss of exon 10
------------------------GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcatgttccttactttgtttggataaatgtagcatatttttctacagaattttgaatttctacgaatggttattgacagttttttgatatttacatag
                        | ||||||||||||||||||||||||||| || ||  ||||||| || || || || ||||| |||| ||  || ||||    |        || |||| |         || |    |  ||   |    |  ||   ||||       |   |    ||    |  |  |     |   |                      
GACCGCGCCAAGCTGCTCAACGTGGTCATGCAGCTGCGCAAGTGCTGCAACCACCCCTACCTGTTCCAGGGCGCGGAGCCCGGCCCGCCCTTCATTACCGgtgtgtgtgcgtgcatgagtgcatgcg----tgcgtgcgaggcactgggggagggacggt--tatatgcccgagcccgacgaagaggggcgcccgagcccgacgaa----------------------

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 425

GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcat ... atttacatagGAAAAATGGTTCTACTAGATAAATTGCTGCCCAAGCTAAAGGAGCGTGATTCCAGAGTCCTAATTTTTTCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcat ... atttacatagGAAAAATGGTTCTACTAGATAAATTGCTGCCCAAGCTAAAGGAGCGTGATTCCAGAGTCCTAATTTTTTCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcat ... atttacatagGAAAAATGGTTCTACTAGATAAATTGCTGCCCAAGCTAAAGGAGCGTGATTCCAGAGTCCTAATTTTTTCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GCCATGCAGCTGCGCAAGTGCTGCAACCATCCATATTTGTTCCAAGGAGCTGAACCTGGCCCACCCTACACAACTGGTGAACATCTAGTTGAGAATGCAGgtaacatcat ... atttacatagGAAAAATGGTTCTACTAGATAAATTGCTGCCCAAGCTAAAGGAGCGTGATTCCAGAGTCCTAATTTTTTCACAG